This core will facilitate studies in most of the collaborative projects and cores by providing expert and high throughput protein analysis for identification and quantification of proteins in complex samples. The core utilizes biochemical protein separation techniques and mass spectrometry as the primary technologies to achieve this goal, and members of this core facility are world leaders in this field. It is the aim of this core to establish a discovery science infrastructure for qualitative and quantitative proteomics at the Institute of Systems Biology. Through interactive collaborations with Glue Grant investigators this core will impact biomedical research in the regulation of the immune response during injury and sepsis. This core facility will permit participants in this grant proposal to 1) rapidly identify unknown proteins, 2) characterize specific post-translational modifications, 3) identify interacting proteins 4) localize protein:protein interaction sites, and 5) quantify the relative abundance of up to thousands of different proteins in complex specimens.